Restrained-Ensemble Molecular Dynamics Simulations Based on Distance Histograms from Double Electron-Electron Resonance Spectroscopy

DEER (double electron electron resonance) spectroscopy is a powerful pulsed ESR (electron spin resonance) technique allowing the determination of spin spin distance histograms between site directed nitroxide label sites on a protein in their native environment However, incorporating ESR/DEER data in structural refinement is challenging because the information from the large number of distance histograms is complex and highly coupled. Here, a novel restrained ensemble molecular dynamics simulation method is developed to incorporate the information from multiple ESR/DEER distance histograms simultaneously. Illustrative tests on three coupled spin labels inserted in T4 lysozyme show that the method efficiently imposes the experimental distance distribution in this system. Different rotameric states of the chi(1) and chi(2) dihedrals in the spin-labels are also explored by restrained ensemble simulations. Using this method, it is hoped that experimental restraints from ESR/DEER experiments can be used to refine structural properties of biological systems.